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r-lib / revdepcheck

R package reverse dependency checking
https://revdepcheck.r-lib.org
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failed to check all packages? #258

Closed bbolker closed 4 years ago

bbolker commented 4 years ago

I'm probably doing something really dumb here, but would appreciate any suggestions. Running revdep_check() on the broom.mixed package (available at github.com:/bbolker/broom.mixed if you want to try) takes about an hour (with no packages initially cached). revdep_report_problems("broom.mixed") reports no problems, but revdep_report_summary("broom.mixed") makes it look like all six of the revdeps failed to check.

Am I missing something obvious? What should I check next?

The failures.md file has sections that look like this ...

# broomExtra
<details>
* Version:
* Source code: ???
* Number of recursive dependencies: 0
Run `revdep_details(,"")` for more info
</details>
## Error before installation
### Devel
### CRAN

revdep_report_summary("broom.mixed"):

# Platform

|field    |value                                              |
|:--------|:--------------------------------------------------|
|version  |R Under development (unstable) (2020-05-14 r78467) |
|os       |Pop!_OS 18.04 LTS                                  |
|system   |x86_64, linux-gnu                                  |
|ui       |X11                                                |
|language |en_US:en                                           |
|collate  |en_US.UTF-8                                        |
|ctype    |en_US.UTF-8                                        |
|tz       |America/Toronto                                    |
|date     |2020-05-16                                         |

# Dependencies

|package     |old   |new         |Δ  |
|:-----------|:-----|:-----------|:--|
|broom.mixed |0.2.5 |0.2.7       |*  |
|dplyr       |NA    |0.8.99.9003 |*  |
|vctrs       |NA    |0.3.0.9000  |*  |

# Revdeps

## Failed to check (6)

|package    |version |error |warning |note |
|:----------|:-------|:-----|:-------|:----|
|broomExtra |?       |      |        |     |
|glmmTMB    |?       |      |        |     |
|gtsummary  |?       |      |        |     |
|huxtable   |?       |      |        |     |
|jtools     |?       |      |        |     |
|nlmixr     |?       |      |        |     |

Session info:

Registered S3 method overwritten by 'devtools':
  method            from       
  print.maintainers revdepcheck
─ Session info ───────────────────────────────────────────────────────────────
 setting  value                                             
 version  R Under development (unstable) (2020-05-14 r78467)
 os       Pop!_OS 18.04 LTS                                 
 system   x86_64, linux-gnu                                 
 ui       X11                                               
 language en_US:en                                          
 collate  en_US.UTF-8                                       
 ctype    en_US.UTF-8                                       
 tz       America/Toronto                                   
 date     2020-05-16                                        

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version    date       lib source                            
 assertthat    0.2.1      2019-03-21 [1] CRAN (R 4.1.0)                    
 backports     1.1.7      2020-05-13 [1] CRAN (R 4.1.0)                    
 base64enc     0.1-3      2015-07-28 [1] CRAN (R 4.1.0)                    
 bit           1.1-15.2   2020-02-10 [1] CRAN (R 4.1.0)                    
 bit64         0.9-7      2017-05-08 [1] CRAN (R 4.1.0)                    
 blob          1.2.1      2020-01-20 [1] CRAN (R 4.1.0)                    
 callr         3.4.3      2020-03-28 [1] CRAN (R 4.1.0)                    
 cli           2.0.2      2020-02-28 [1] CRAN (R 4.1.0)                    
 clisymbols    1.2.0      2017-05-21 [1] CRAN (R 4.1.0)                    
 crancache     0.0.0.9001 2020-04-18 [1] Github (r-lib/crancache@7ea4e47)  
 cranlike      1.0.2      2018-11-26 [1] CRAN (R 4.1.0)                    
 crayon        1.3.4.9000 2020-05-09 [1] Github (r-lib/crayon@dcf6d44)     
 curl          4.3        2019-12-02 [1] CRAN (R 4.1.0)                    
 DBI           1.1.0      2019-12-15 [1] CRAN (R 4.1.0)                    
 debugme       1.1.0      2017-10-22 [1] CRAN (R 4.1.0)                    
 desc          1.2.0      2018-05-01 [1] CRAN (R 4.1.0)                    
 devtools      2.3.0      2020-04-10 [1] CRAN (R 4.1.0)                    
 digest        0.6.25     2020-02-23 [1] CRAN (R 4.1.0)                    
 ellipsis      0.3.1      2020-05-15 [1] CRAN (R 4.1.0)                    
 fansi         0.4.1      2020-01-08 [1] CRAN (R 4.1.0)                    
 fs            1.4.1      2020-04-04 [1] CRAN (R 4.1.0)                    
 glue          1.4.1      2020-05-13 [1] CRAN (R 4.1.0)                    
 gmailr        1.0.0      2019-08-23 [1] CRAN (R 4.1.0)                    
 hms           0.5.3      2020-01-08 [1] CRAN (R 4.1.0)                    
 httr          1.4.1      2019-08-05 [1] CRAN (R 4.1.0)                    
 jsonlite      1.6.1      2020-02-02 [1] CRAN (R 4.1.0)                    
 knitr         1.28       2020-02-06 [1] CRAN (R 4.1.0)                    
 lifecycle     0.2.0      2020-03-06 [1] CRAN (R 4.1.0)                    
 magrittr      1.5        2014-11-22 [1] CRAN (R 4.1.0)                    
 memoise       1.1.0      2017-04-21 [1] CRAN (R 4.1.0)                    
 parsedate     1.2.0      2019-05-08 [1] CRAN (R 4.1.0)                    
 pillar        1.4.4      2020-05-05 [1] CRAN (R 4.1.0)                    
 pkgbuild      1.0.8      2020-05-07 [1] CRAN (R 4.1.0)                    
 pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 4.1.0)                    
 pkgload       1.0.2      2018-10-29 [1] CRAN (R 4.1.0)                    
 prettyunits   1.1.1      2020-01-24 [1] CRAN (R 4.1.0)                    
 processx      3.4.2      2020-02-09 [1] CRAN (R 4.1.0)                    
 progress      1.2.2      2019-05-16 [1] CRAN (R 4.1.0)                    
 ps            1.3.3      2020-05-08 [1] CRAN (R 4.1.0)                    
 R6            2.4.1      2019-11-12 [1] CRAN (R 4.1.0)                    
 rappdirs      0.3.1      2016-03-28 [1] CRAN (R 4.1.0)                    
 rcmdcheck     1.3.3.9000 2020-04-18 [1] Github (r-lib/rcmdcheck@1484bed)  
 Rcpp          1.0.4.6    2020-04-09 [1] CRAN (R 4.1.0)                    
 rematch2      2.1.2      2020-05-01 [1] CRAN (R 4.1.0)                    
 remotes       2.1.1      2020-02-15 [1] CRAN (R 4.1.0)                    
 revdepcheck * 1.0.0.9001 2020-04-18 [1] Github (r-lib/revdepcheck@04115d6)
 rlang         0.4.6      2020-05-02 [1] CRAN (R 4.1.0)                    
 rprojroot     1.3-2      2018-01-03 [1] CRAN (R 4.1.0)                    
 RSQLite       2.2.0      2020-01-07 [1] CRAN (R 4.1.0)                    
 sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 4.1.0)                    
 testthat      2.3.2      2020-03-02 [1] CRAN (R 4.1.0)                    
 tibble        3.0.1      2020-04-20 [1] CRAN (R 4.1.0)                    
 usethis       1.6.1      2020-04-29 [1] CRAN (R 4.1.0)                    
 vctrs         0.3.0.9000 2020-05-12 [1] Github (r-lib/vctrs@4ff6b79)      
 whoami        1.3.0      2019-03-19 [1] CRAN (R 4.1.0)                    
 withr         2.2.0      2020-04-20 [1] CRAN (R 4.1.0)                    
 xfun          0.13       2020-04-13 [1] CRAN (R 4.1.0)                    
 xopen         1.0.0      2018-09-17 [1] CRAN (R 4.1.0)                    
 yaml          2.2.1      2020-02-01 [1] CRAN (R 4.1.0)                    

[1] /usr/local/lib/R/site-library
[2] /usr/local/lib/R/library
>
bbolker commented 4 years ago

update: I'm somehow getting packages installed with the wrong R version, so that I'm getting errors like

Error: package ‘minqa’ was installed before R 4.0.0: please re-install it

even though I've tried to make sure that the right R version was used. (R version 3.6.3 does exist in the regular system location /usr/local/bin/R; I thought I had my path set correctly but will keep trying ...

Further information: if I navigate directly to the location where the dependencies are installed (e.g. /home/bbolker/lme4/revdep/library/AICcmodavg/minqa/Meta I find an ancient version. I'm suspecting some kind of crancache problem, will keep digging ...

 readRDS("package.rds")$Built
$R
[1] ‘3.5.0’

$Platform
[1] "x86_64-pc-linux-gnu"

$Date
[1] "2017-11-08 21:03:30 UTC"

$OStype
[1] "unix"
bbolker commented 4 years ago

Pretty sure this was a crancache problem.